3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-1122

Visualizing tmRNA entry into a stalled ribosome.

by single particle reconstruction, at 13 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 42, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 42, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-1zc8, Surface level: 42, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-1zc8, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1122
TitleVisualizing tmRNA entry into a stalled ribosome.
Mapthis is a ribosome consisting 70S + Psite tRNA + mRNA + EF-Tu.GDP + alanylated tmRNA + SmpB + Kirromycin + S1
Sample70S-Psite tRNA - mRNA - EF-Tu.GDP - alanylated tmRNA - SmpB - Kirromycin - S1
AuthorsValle M, Gillet R, Kaur S, Henne A, Ramakrishnan V, Frank J
DateDeposition: 2005-03-24, Header release: 2005-04-11, Map release: 2005-04-11, Last update: 2012-10-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 42, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 42, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-1zc8, Surface level: 42, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-1zc8, Image by Jmol

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-1zc8

CiteFit

Cite: data citing same article

Fit: output model of fitting

Similar strucutres
List of similar structure data Omokage searchabout Omokage system
Article
Citation - Primary
ArticleScience, Vol. 300, Issue 5616, Page 127-30, Year 2003
TitleVisualizing tmRNA entry into a stalled ribosome.
AuthorsMikel Valle, Reynald Gillet, Sukhjit Kaur, Anke Henne, V Ramakrishnan, Joachim Frank
Howard Hughes Medical Institute, Wadsworth Center, Health Research, Inc., Empire State Plaza, Albany, NY 12201-0509, USA.
KeywordsAlanine, Anticodon, Bacterial Proteins (metabolism), Codon, Codon, Terminator, Cryoelectron Microscopy, Guanosine Triphosphate (metabolism, 86-01-1), Image Processing, Computer-Assisted, Models, Molecular, Nucleic Acid Conformation, Open Reading Frames, Peptide Elongation Factor Tu (metabolism, 3.6.1.-), Protein Biosynthesis, Pyridones (pharmacology), RNA, Bacterial (chemistry), RNA, Messenger (chemistry), RNA, Transfer (chemistry, 9014-25-9), RNA-Binding Proteins (chemistry), Ribosomal Proteins (chemistry), Ribosomes (metabolism), Thermus thermophilus (chemistry), mocimycin, ribosomal protein S1, small protein B, tmRNA
LinksPubMed: 12677067, DOI: 10.1126/science.1081798
Map
Fileemd_1122.map.gz ( map file in CCP4 format, 10720 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
140 pix
2.82 A/pix
= 394.8 A
140 pix
2.82 A/pix
= 394.8 A
140 pix
2.82 A/pix
= 394.8 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:54.9, 42 (movie #1):
Minimum - Maximum: -147.485 - 313.886
Average (Standard dev.): 2.87458 (28.7702)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions140140140
Origin-70-70-70
Limit696969
Spacing140140140
Unit CellA= B= C: 394.8 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.82 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.822.822.82
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z394.800394.800394.800
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-220-220-220
NX/NY/NZ441441441
MAP C/R/S123
start NC/NR/NS-70-70-70
NC/NR/NS140140140
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-147.485313.8862.875
Annotation Detailsthis is a ribosome consisting 70S + Psite tRNA + mRNA + EF-Tu.GDP + alanylated tmRNA + SmpB + Kirromycin + S1
Supplement
Images
Images
Sample
Name70S-Psite tRNA - mRNA - EF-Tu.GDP - alanylated tmRNA - SmpB - Kirromycin - S1
Number of Components5
Component #1: ribosome-prokaryote - 70S Ribosome
Scientific name70S Ribosome
DetailsThermus thermophilus
Scientific Name of SpeciesThermus thermophilus HB8
NCBI taxonomy300852
ProkaryoteALL
Recombinant expressionNo
Component #2: nucleic-acid - tRNA
Scientific nametRNA
DetailsP site
Scientific Name of SpeciesThermus thermophilus HB8
NCBI taxonomy300852
SyntheticNo
StructureSINGLE STRANDED
ClassT-RNA
Component #3: protein - EF-Tu
Scientific nameEF-Tu
Scientific Name of SpeciesThermus thermophilus HB8
NCBI taxonomy300852
Recombinant expressionNo
Component #4: ligand - tmRNA
Scientific nametmRNA
Scientific Name of SpeciesThermus thermophilus HB8
NCBI taxonomy300852
Recombinant expressionNo
Component #5: protein - SmpB
Scientific nameSmpB
Scientific Name of SpeciesThermus thermophilus HB8
NCBI taxonomy300852
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Stateparticle
BufferDetails: 25 mM Hepes-KOH pH 7.5, 30 mM NH4Cl, 7mM MgCl2, 2 mM ATP, 6 mM PEP, 10g/ml PK
pH: 7.5
Vitrification
Cryogen NameETHANE
Humidity90
Temperature93 Kelvin
InstrumentHOMEMADE PLUNGER
MethodBlot for 2 seconds before plunging
DetailsVitrification instrument: two side blotting plunger
Imaging
MicroscopeFEI TECNAI F20
Date2002-8-1
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 49000, Calibrated: 52000
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1450 nm - 3700 nm
Specimen Holder
HolderCryo transfer
ModelGATAN LIQUID NITROGEN
Temperature93 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
Number of Digital Images44
Sampling Size14
Od Range1.2
Quant Bit Number12
ScannerZEISS SCAI
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmreference projection
SoftwareSPIDER
CTF Correctiondefocus groups
Resolution By Author13 A
Resolution MethodFSC at 0.15 cut-off
Euler Angles DetailsSPIDER definition
Single Particle
Number of Projections27644
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Model #0
Refinement Protocolrigid body
Target Criteriacross correlation coefficient
Softwaremanual
DetailsProtocol: Rigid Body. The domains were separately fitted by manual docking using program O
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1122.xml (9.2 KB)
Map dataemd_1122.map.gz (9.9 MB)
Images1122.gif (15.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1122
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 26.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 26.5 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 207.6 KB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.5 MB